Molecubotics assembler parts ideas

In our roadmap we classified the parts needed by an assembler into several
kinds:

structural framework

flexible joints

actuators

grippers

joining tools

We also described how basic design decisions about gripping method and
joining method are coupled: one scheme is for the assembler's gripper to
hold a new MBB in place while a joining tool catalyzes the formation of a
strong bond to the workpiece, allowing the gripper to release the MBB
simply by pulling away with enough strength; another scheme is for the
gripper to reduce its affinity and retract even while the MBB is only
weakly joined to the workpiece, and later to strengthen many MBB-workpiece
bonds at once, perhaps by altering the chemical conditions in the
solution.

The choice of permanent bonding method between the MBBs is the design
issue of greatest uncertainty at the moment. In our internal planning that
means we should work on it first, but to explain the choices we've already
made, I should start by explaining the easier ones.

1 (structure). We think that pure-DNA structures of the kind pioneered by
Seeman are sufficient by themselves to form most or all structural
components of a primitive assembler. They are certainly able (in
principle) to produce a sufficient variety and complexity of forms, so the
only remaining issue is whether their stiffness is adequate to reliably
separate the internal parts or objects they are holding which should not
touch each other. (Some floppiness is fine, and will actually help the
bonding of MBBs to the workpiece, as long as it is not so much that a new
MBB can be bonded to the wrong existing MBB in the workpiece being
formed.)

The tests of stiffness of the DX and TX motifs, published by Seeman,
already support the idea that they are stiff enough. (These tests consist
of producing long beams, whose ends could in principle form covalent bonds
to one another if they came near enough, and testing whether they do in
fact form those bonds. Similar tests can be performed on substructures
intended to be parts of an assembler.)

The general principle that thicker beams are much stiffer also will apply
in this case.

1b. If, for some reason in spite of the above arguments, pure-DNA
structures are not stiff enough, we would want to augment our set of MBBs
by some kind of much stiffer rod. (And, eventually, we'd want to do this
anyway, to open up new applications requiring more stiffness in the
assembler than whatever it needed to reproduce itself.)

There are natural protein rods that are quite stiff, including some virus
coats (which are also quite thick, but would still be usable). The one
with the longest persistence length is actin, a linear polymer of two
protein subunits which has a persistence length of more than a micron, and
is quite thin. It's part of muscle, and is also used inside cells for
various purposes related to motion and stiffness. To use actin as the
basis of short rod-like MBBs for nanomachines, we'd need to develop a way
to make actin rods of a desired length, preferably with specific DNA
sequences attached at the ends and maybe at specific points along the rod.
We have some ideas for doing this - contact us if you are interested.

It is also conceivable to stiffen DNA structures by incorporating other
organic molecules into them which can produce covalent crosslinks.
Bergstrom has designed and incorporated custom organic molecules into DNA
with the idea of linking neighboring dsDNA domains (double helices),
though I don't believe he actually demonstrated linking them (and he told
me his grant applications to pursue this were rejected -- that was several
years ago); Glick has incorporated bases containing -SH groups into DNA,
which when oxidized produce a "disulfide base pair" (whose overall shape
is compatible with that of a standard Watson-Crick base pair, so the dsDNA
is not distorted) which makes a single dsDNA domain stiffer. Glen
Research, which offers a catalog of about 60 modified bases that can be
incorporated into DNA, told me it could synthesize a custom one (from an
existing published protocol, like that of Glick's) for about $1500.

1c. If stiffness is still an issue, there are several other potential ways
to improve it, but they're all harder. But
we'd be surprised if the above-described methods weren't sufficient. Once
we have a chance to produce a detailed design of a prototype assembler on
which to do a mechanical analysis and/or simulation (after seed funding,
but long before trying to build one), we'll have much better evidence for
this claim.

2. For flexible joints, we can in most cases just provide fewer
connections between structural parts, leaving them with some freedom of
motion, since the individual connections will not be very rigid.

Whenever a single tether-like connection is used (whether short or long),
we have a fully flexible joint.

For the assembler to work, its main operation is to bring some molecular
surface into some range of possible positions and orientations, letting
the natural affinity of the structure of that surface provide the finest
positional control, so "tethering" (with short tethers) will often be
adequate.

Single-stranded DNA is a very flexible tether. Several other flexible
linear polymers can be chemically joined to DNA if they make better
tethers for some purposes (for example, if the negative charge of DNA
makes it undesirable).

So we don't consider flexible joints to be a problem.

3 (actuators). Our DNA actuator design will be sufficient for controlling
the first assembler, since it provides an almost unlimited number of
independent degrees of freedom (by means of variants which can be
independently controlled), each with a modulatable tensile force several
times higher than that required to pull apart dsDNA (and which can be
increased by using more than one actuator in parallel), and an estimated
reaction speed of no worse than 30 seconds (the demonstrated speed of
Bernie Yurke's related actuator), which is compatible with performing
hundreds of sequential operations on a reasonable timescale, and which can
probably be highly optimized.

Ultimately we would also like to develop faster actuators, and there are
many possible ways to do this. One of the simplest was
reported
by John Gaynor at the most recent Foresight
Molecular Nanotechnology conference, in which a specific protein's
affinity for DNA is modulated by a small organic ligand. There are also
possibilities for actuators controlled by something other than a dissolved
chemical species. But none of these will be a requirement for making the
first functioning assembler.

4 (grippers). It is likely that DNA hybridization alone will be sufficient
for making an assembler per se, which assembles MBBs with specific DNA
sequences already attached, which are used only for allowing the assembler
to grip them in a controlled orientation.

For many applications, we'd like to grip a more general class of object,
such as the small organic molecules which have been developed as possible
electronic switching components. The most obvious (and best developed)
method is to use a protein-based receptor, or possibly an RNA-based
receptor, with complementary shape and charge to the object to be gripped.
It has been possible for many years to induce animals to develop
antibodies to a variety of targets, and more recently several other
methods have been developed for creating peptides with high affinities to
specific targets, such as phage display. This seems to be a mature
technology, and is within the area of expertise of one of our informal
advisors, and his company.

Recent announced developments have included peptides with a high and
specific affinity for silicon and for certain metals (a different peptide
specific for each one). These would be directly useful for certain
applications, and they add to the long list of reported successes in
development of molecules with specific desired affinities.

More speculatively, but quite feasibly, it should be possible to use
similar methods to develop peptides whose affinity for some target was
high only when, for example, some metal ion was present (as is the case
for natural "zinc finger" proteins, and for the "6-His" tags which are
used commercially for separating synthetic proteins from mixtures in a
nickel- dependent way). This could probably be used to develop peptides
which gripped specific targets with a modulatable affinity, if this
capability was necessary.

5 (joining tools). There are several possible solutions for the system
used to permanently join MBBs in the first assembler and in its first
products, and we don't yet know which one will prove simplest. For any of
them, we would need to augment our set of scientific advisors by at least
one chemist, and one specialist in whatever technique we would use for
developing the joining tool. (In the case of artificial evolution of
protein enzymes, such a specialist has already informally offered to be
our scientific advisor.)

a. The ideal solution for many applications would be to form covalent
bonds between specific organic moieties (molecular fragments) designed
into the MBBs we wanted to assemble, or naturally present in them, and to
catalyze the formation of these bonds by an enzymatic "tool" held in place
by the assembler, so that no special provisions would be required to keep
the rate of "accidental" bonding of MBBs very low, even when new MBBs
introduced into solution had not yet been adsorbed onto the gripper's
receptor for them.

One strategy for this would be to develop a new protein enzyme which
catalyzed the formation of a suitable bond. To do this, we'd study the
known natural enzymes which catalyze related reactions, and with the help
of expert advice from a chemist, choose some which might serve our
purposes. Then we would contract with a company which artificially evolves
improvements to natural proteins by generating and testing lots of
modifications to the gene that codes for them. I have asked the CEO of one
such company how feasible that sounds to him, and what it would cost. He
says that, once the natural protein to modify is chosen and a test for its
effectiveness exists, optimizing it by artificial evolution takes 6 months
and costs $500,000. If the protein already catalyzes the desired reaction
on small substrates but has to be modified in order to remove steric
constraints so it will work on extended structures, then he is not aware
of this kind of modification having been tried, but he sees no fundamental
obstacle to its working, so if several were tried, it it reasonable to
suppose that one would work.

In fact, just a few months ago there was a rationally designed
modification to a catalytic protein reported
here which
modified its substrate specificity in a similar way. This modification
consisted of changing the shape of a "pocket" into which the substrate
should fit, near the part of the substrate modified by the reaction. This
can be thought of as "proof of concept research" along these lines.

b. There have recently been several "dna enzymes" produced by artificial
evolution of DNA sequences which hold a metal ion in a way which forms a
catalytic center. The developer of these thinks they can be applied as
very sensitive detectors of the metal cofactor. The same technique could
presumably also be applied to produce metal-containing DNA enzymes to
catalyze a desired reaction which was already known to be catalyzed by
that metal in a less specific way under other conditions.

c. We could choose organic groups which readily form covalent bonds under
suitable conditions, with no need for catalysis. There are several
possible choices, including disulfide bonds (though we'd want a better
chemist advisor to help us pick the best choices to actually try). The
problem here is that the reactions are slow, so we'd want the assembler to
have some way of temporarily fixing several MBBs into place before joining
all of them at once. That way might consist of any of the weaker
fast-forming bonds I'll mention next.

d. Especially for the first assembler, we might not need the strength of
covalent bonds, either because weaker ones were sufficient for the
expected operating forces and design lifetime, or because we would use
several in parallel when greater strength was required. (It is worth
noting that most large structures in living organisms are held together
with non-covalent bonds.)

There are several kinds of non-covalent bonds to make use of, some of
which form very quickly. I've already mentioned bonds between peptides
which form around coordinated metal ions such as nickel. There is also DNA
hybridization itself, which can be quite permanent for sufficiently long
DNA sequences in the right solutions. There are variants of DNA, namely
PNA, which form stronger bonds which (unlike DNA) don't depend on the salt
concentration for their strength. And there are high-affinity bonds
between peptides or proteins and other proteins or a variety of other
molecules, the strongest of which is between biotin (a small molecule
often built into synthetic DNA) and avidin (a natural protein readily
available commercially).